Figure 5.

Divergent translational and transcriptional regulation for cRPs and hexose during adaptation to high NaCl. (A–D) A subset of genes are differently regulated on the level of total mRNA and on the level of polysome association. (A) To identify major functional differences between polysomal and the total mRNA salt regulation, the overrepresentation of known cellular functions among the top 200 most salt-induced (left panel) genes in each of wt (2, 6, and 30 min), hog1Δ (6 min), and rck2Δ cells (6 min). Colors indicate log₍₂₎ fold enrichment in each class for functional categories that deviated significantly from the chance expectation at p < 10⁻⁴ (Fisher's exact test) in at least one class. Yellow, functional overrepresentation; blue, functional underrepresentation. Functional annotations were taken from the MIPS S. cerevisiae genome database, including only categories with at least 15 members present in the screen. All enriched categories were hierarchically clustered according to degree of enrichment in each class using an uncentered Pearson similarity metric and average linkage mapping. Blue text, counterdirectional functional enrichments for total and polysome-associated mRNA; red text, Hog1 dependent functional enrichments. (B and D) The difference in the degree of salt induction on the polysomal association level and the total mRNA level (log₂ [polysome NaCl induction/total mRNA NaCl induction]) was calculated for each individual transcript. (B) All genes annotated as associated with ribosomes were hierarchically clustered (as above) according to the difference in degree of translational and transcriptional induction (log₂ [polysome NaCl induction/total mRNA NaCl induction]). Red squares, higher translational than transcriptional induction and green squares, the converse. Major clustering groups and the relative proportions (absolute numbers within brackets) of gene products in each clustering group that are resident members of the mitochondrial ribosome, the cytoplasmic ribosome, or more loosely associated with the cytoplasmic ribosome are indicated with color. A subset of mRNAs encoding cRPs is more strongly induced on the translational level (red lines). (C) Membrane protein–encoding transcripts are more frequent among the polysome association salt-induced transcripts than among the total mRNA salt-induced transcripts. Degree of enrichment of membrane proteins (GO annotations) among the top 25, 50, 100, and 200 most salt-induced transcripts considering either polysomal association induced or total mRNA–induced transcripts in wt cells. Enrichments are significantly stronger on the level of polysomal association among the very highly salt-induced genes (Student's t test; **p < 0.01, ***p < 0.001). (D) All genes annotated (MIPS FunCat) as possessing sugar transport activity was hierarchically clustered (as above) according to the difference in degree of salt induction on the polysomal association level and the total mRNA level (log₂ [polysome salt induction/total mRNA salt induction]). Major clustering groups are indicated with color. A subset of sugar transport genes with primarily low affinity hexose transport activity is more strongly salt-induced on the polysomal level (red lines).